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Genome-wide association study

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https://www.readbyqxmd.com/read/28453904/genetics-and-other-factors-in-the-aetiology-of-female-pattern-hair-loss
#1
REVIEW
Silke Redler, Andrew G Messenger, Regina C Betz
Pattern hair loss is the most common form of hair loss in both women and men. Male pattern hair loss, also termed male androgenetic alopecia (M-AGA), is an androgen-dependent trait that is predominantly genetically determined. Androgen-mediated mechanisms are probably involved in FPHL in some women but the evidence is less strong than in M-AGA; and other non-androgenic pathways, including environmental influences, may contribute to the aetiology. Genome-wide association studies (GWASs) have identified several genetic loci for M-AGA and have provided better insight into the underlying biology...
April 28, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/28453673/vexor-an-integrative-environment-for-prioritization-of-functional-variants-in-fine-mapping-analysis
#2
Audrey Lemaçon, Charles Joly Beauparlant, Penny Soucy, Jamie Allen, Douglas Easton, Peter Kraft, Jacques Simard, Arnaud Droit
Motivation: The identification of the functional variants responsible for observed genome-wide association studies (GWAS) signals is one of the most challenging tasks of the post-GWAS research era. Several tools have been developed to annotate genetic variants by their genomic location and potential functional implications. Each of these tools has its own requirements and internal logic, which forces the user to become acquainted with each interface. Results: From an awareness of the amount of work needed to analyze a single locus, we have built a flexible, versatile and easy-to-use web interface designed to help in prioritizing variants and predicting their potential functional implications...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453575/genome-wide-association-study-of-red-blood-cell-traits-in-hispanics-latinos-the-hispanic-community-health-study-study-of-latinos
#3
Chani J Hodonsky, Deepti Jain, Ursula M Schick, Jean V Morrison, Lisa Brown, Caitlin P McHugh, Claudia Schurmann, Diane D Chen, Yong Mei Liu, Paul L Auer, Cecilia A Laurie, Kent D Taylor, Brian L Browning, Yun Li, George Papanicolaou, Jerome I Rotter, Ryo Kurita, Yukio Nakamura, Sharon R Browning, Ruth J F Loos, Kari E North, Cathy C Laurie, Timothy A Thornton, Nathan Pankratz, Daniel E Bauer, Tamar Sofer, Alex P Reiner
Prior GWAS have identified loci associated with red blood cell (RBC) traits in populations of European, African, and Asian ancestry. These studies have not included individuals with an Amerindian ancestral background, such as Hispanics/Latinos, nor evaluated the full spectrum of genomic variation beyond single nucleotide variants. Using a custom genotyping array enriched for Amerindian ancestral content and 1000 Genomes imputation, we performed GWAS in 12,502 participants of Hispanic Community Health Study and Study of Latinos (HCHS/SOL) for hematocrit, hemoglobin, RBC count, RBC distribution width (RDW), and RBC indices...
April 28, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28453389/gwas-analysis-of-treatment-resistant-schizophrenia-interaction-effect-of-childhood-trauma
#4
Arthur Koga, Ali Bani-Fatemi, Nuwan Hettige, Carol Borlido, Clement Zai, John Strauss, Philip Gerretsen, Ariel Graff, Gary Remington, Vincenzo De Luca
AIMS: In the current study, we aimed to compare the prevalence of adverse lifetime events in treatment resistant and non-treatment resistant schizophrenia in a genome-wide association study. MATERIALS & METHODS: Our sample consisted of 84 Caucasian participants with schizophrenia spectrum disorders, assessed cross-sectionally to collect information regarding drug effectiveness and childhood trauma. Using a genome-wide association analysis, we tested single-nucleotide polymorphisms for their association with resistance to antipsychotics defined according to American Psychiatric Association criteria...
April 28, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28449094/hepatic-tm6sf2-overexpression-affects-cellular-apob-trafficking-plasma-lipid-levels-hepatic-steatosis-and-atherosclerosis
#5
Nicole Ehrhardt, Michael E Doche, Shuang Chen, Hui Z Mao, Meghan T Walsh, Candy Bedoya, Maha Guindi, Weidong Xiong, Joseph Ignatius Irudayam, Jahangir Iqbal, Sebastien Fuchs, Samuel W French, M Mahmood Hussain, Moshe Arditi, Vaithilingaraja Arumugaswami, Miklós Péterfy
The human TM6SF2 gene has been implicated in plasma lipoprotein metabolism, alcoholic and non-alcoholic fatty liver disease and myocardial infarction in multiple genome-wide association studies. To investigate the role of Tm6sf2 in metabolic homeostasis, we generated mice with elevated expression using adeno-associated virus (AAV)-mediated gene delivery. Hepatic overexpression of mouse Tm6sf2 resulted in phenotypes previously observed in Tm6sf2-deficient mice including reduced plasma lipid levels, diminished hepatic TG secretion and increased hepatosteatosis...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28449091/gwab-a-web-server-for-the-network-based-boosting-of-human-genome-wide-association-data
#6
Jung Eun Shim, Changbae Bang, Sunmo Yang, Tak Lee, Sohyun Hwang, Chan Yeong Kim, U Martin Singh-Blom, Edward M Marcotte, Insuk Lee
During the last decade, genome-wide association studies (GWAS) have represented a major approach to dissect complex human genetic diseases. Due in part to limited statistical power, most studies identify only small numbers of candidate genes that pass the conventional significance thresholds (e.g. P ≤ 5 × 10-8). This limitation can be partly overcome by increasing the sample size, but this comes at a higher cost. Alternatively, weak association signals can be boosted by incorporating independent data. Previously, we demonstrated the feasibility of boosting GWAS disease associations using gene networks...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449029/a-genome-wide-association-study-identifies-nucleotide-variants-at-siglec5-and-defa1a3-as-risk-loci-for-periodontitis
#7
Matthias Munz, Christina Willenborg, Gesa M Richter, Yvonne Jockel-Schneider, Christian Graetz, Ingmar Staufenbiel, Jürgen Wellmann, Klaus Berger, Bastian Krone, Per Hoffmann, Nathalie van der Velde, André G Uitterlinden, Lisette C P G M de Groot, Amr Sawalha, Haner Direskeneli, Güher Saruhan-Direskeneli, Esra Guzeldemir-Akcakanat, Gencay Keceli, Matthias Laudes, Barbara Noack, Alexander Teumer, Birte Holtfreter, Thomas Kocher, Peter Eickholz, Jörg Meyle, Christof Doerfer, Corinna Bruckmann, Wolfgang Lieb, Andre Franke, Stefan Schreiber, Rahime M Nohutcu, Jeanette Erdmann, Bruno G Loos, Soeren Jepsen, Henrik Dommisch, Arne S Schaefer
Periodontitis is one of the most common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an estimated heritability of 50%. The disease is characterized by destruction of the alveolar bone due to an aberrant host inflammatory response to a dysbiotic oral microbiome. Previous genome-wide association studies (GWAS) have reported several suggestive susceptibility loci. Here, we conducted a GWAS using a German and Dutch case-control sample of aggressive periodontitis (AgP, 896 cases, 7,104 controls), a rare but highly severe and early-onset form of periodontitis, validated the associations in a German sample of severe forms of the more moderate phenotype chronic periodontitis (CP) (993 cases, 1,419 controls)...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28448896/differentially-methylated-embryonal-fyn-associated-substrate-efs-gene-as-a-blood-specific-epigenetic-marker-and-its-potential-application-in-forensic-casework
#8
Athina Vidaki, Cecilia Johansson, Federica Giangasparo
DNA methylation patterns have the ability to reveal the activities of genes within a certain tissue at a particular time point. Tissue-specific DNA methylation patterns have been previously investigated for their applicability in the identification of forensically relevant body fluids, however there is still a lack in robust markers. While following a genome-wide scale investigation has a great potential to reveal useful tissue-specific changes, a gene-targeted approach can also lead to significant outcomes, especially in genomic locations not included in the genome-wide experiments...
April 19, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28448534/intense-light-elicited-upregulation-of-mir-21-facilitates-glycolysis-and-cardioprotection-through-per2-dependent-mechanisms
#9
Colleen Marie Bartman, Yoshimasa Oyama, Kelley Brodsky, Ludmila Khailova, Lori Walker, Michael Koeppen, Tobias Eckle
A wide search for ischemic preconditioning (IPC) mechanisms of cardioprotection identified the light elicited circadian rhythm protein Period 2 (Per2) to be cardioprotective. Studies on cardiac metabolism found a key role for light elicited Per2 in mediating metabolic dependence on carbohydrate metabolism. To profile Per2 mediated pathways following IPC of the mouse heart, we performed a genome array and identified 352 abundantly expressed and well-characterized Per2 dependent micro RNAs. One prominent result of our in silico analysis for cardiac Per2 dependent micro RNAs revealed a selective role for miR-21 in the regulation of hypoxia and metabolic pathways...
2017: PloS One
https://www.readbyqxmd.com/read/28447668/functional-characterization-of-a-multi-cancer-risk-locus-on-chr5p15-33-reveals-regulation-of-tert-by-znf148
#10
Jun Fang, Jinping Jia, Matthew Makowski, Mai Xu, Zhaoming Wang, Tongwu Zhang, Jason W Hoskins, Jiyeon Choi, Younghun Han, Mingfeng Zhang, Janelle Thomas, Michael Kovacs, Irene Collins, Marta Dzyadyk, Abbey Thompson, Maura O'Neill, Sudipto Das, Qi Lan, Roelof Koster, Rachael S Stolzenberg-Solomon, Peter Kraft, Brian M Wolpin, Pascal W T C Jansen, Sara Olson, Katherine A McGlynn, Peter A Kanetsky, Nilanjan Chatterjee, Jennifer H Barrett, Alison M Dunning, John C Taylor, Julia A Newton-Bishop, D Timothy Bishop, Thorkell Andresson, Gloria M Petersen, Christopher I Amos, Mark M Iles, Katherine L Nathanson, Maria Teresa Landi, Michiel Vermeulen, Kevin M Brown, Laufey T Amundadottir
Genome wide association studies (GWAS) have mapped multiple independent cancer susceptibility loci to chr5p15.33. Here, we show that fine-mapping of pancreatic and testicular cancer GWAS within one of these loci (Region 2 in CLPTM1L) focuses the signal to nine highly correlated SNPs. Of these, rs36115365-C associated with increased pancreatic and testicular but decreased lung cancer and melanoma risk, and exhibited preferred protein-binding and enhanced regulatory activity. Transcriptional gene silencing of this regulatory element repressed TERT expression in an allele-specific manner...
May 2, 2017: Nature Communications
https://www.readbyqxmd.com/read/28447608/common-variants-in-zmiz1-and-near-ngf-confer-risk-for-primary-dysmenorrhoea
#11
Zhiqiang Li, Jianhua Chen, Ying Zhao, Yujiong Wang, Jinrui Xu, Jue Ji, Jingyi Shen, Weiping Zhang, Zuosong Chen, Qilin Sun, Lijuan Mao, Shulin Cheng, Bo Yang, Dongtao Zhang, Yufeng Xu, Yingying Zhao, Danping Liu, Yinhuan Shen, Weijie Zhang, Changgui Li, Jiawei Shen, Yongyong Shi
Primary dysmenorrhoea, defined as painful menstrual cramps in the absence of pelvic pathology, is a common problem in women of reproductive age. Its aetiology and pathophysiology remain largely unknown. Here we performed a two-stage genome-wide association study and subsequent replication study to identify genetic factors associated with primary dysmenorrhoea in a total of 6,770 Chinese individuals. Our analysis provided evidence of a significant (P<5 × 10(-8)) association at rs76518691 in the gene ZMIZ1 and at rs7523831 near NGF...
April 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28447399/genome-wide-association-study-of-hiv-associated-neurocognitive-disorder-hand-a-charter-group-study
#12
Peilin Jia, Zhongming Zhao, Todd Hulgan, William S Bush, David C Samuels, Cinnamon S Bloss, Robert K Heaton, Ronald J Ellis, Nicholas Schork, Christina M Marra, Ann C Collier, David B Clifford, Benjamin B Gelman, Ned Sacktor, Susan Morgello, David M Simpson, J Allen McCutchan, Jill S Barnholtz-Sloan, Donald R Franklin, Debralee Rosario, Scott L Letendre, Igor Grant, Asha R Kallianpur
HIV-associated neurocognitive disorder (HAND) often complicates HIV infection despite combination antiretroviral therapy (ART) and may be influenced by host genomics. We performed a genome-wide association study (GWAS) of HAND in 1,050 CNS HIV Anti-Retroviral Therapy Effects Research (CHARTER) Study participants. All participants underwent standardized, comprehensive neurocognitive, and neuromedical assessments to determine if they had cognitive impairment as assessed by the Global Deficit Score (GDS), and individuals with comorbidities that could confound diagnosis of HAND were excluded...
April 26, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28447115/human-genetics-as-a-model-for-target-validation-finding-new-therapies-for-diabetes
#13
REVIEW
Soren K Thomsen, Anna L Gloyn
Type 2 diabetes is a global epidemic with major effects on healthcare expenditure and quality of life. Currently available treatments are inadequate for the prevention of comorbidities, yet progress towards new therapies remains slow. A major barrier is the insufficiency of traditional preclinical models for predicting drug efficacy and safety. Human genetics offers a complementary model to assess causal mechanisms for target validation. Genetic perturbations are 'experiments of nature' that provide a uniquely relevant window into the long-term effects of modulating specific targets...
April 26, 2017: Diabetologia
https://www.readbyqxmd.com/read/28446795/variants-in-the-il7ra-gene-confer-susceptibility-to-multiple-sclerosis-in-caucasians-evidence-based-on-9734-cases-and-10436-controls
#14
Hong Liu, Jian Huang, Mengmeng Dou, Yong Liu, Biying Xiao, Xu Liu, Zunnan Huang
Recently, numerous genome wide association studies (GWAS) and other case-control association studies examining the relationship between interleukin-7 receptor α chain (IL7RA) gene rs3194051, rs987107, rs11567686, and rs11567685 variants and multiple sclerosis (MS) risk have been conducted, but the conclusions have been inconsistent. The main objective of this meta-analysis was to more precisely explore the association of these four IL7RA variants with MS development. Twenty-seven eligible studies involving 9734 cases and 10436 controls were included in the present meta-analysis...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446202/analyzing-the-genes-related-to-alzheimer-s-disease-via-a-network-and-pathway-based-approach
#15
Yan-Shi Hu, Juncai Xin, Ying Hu, Lei Zhang, Ju Wang
BACKGROUND: Our understanding of the molecular mechanisms underlying Alzheimer's disease (AD) remains incomplete. Previous studies have revealed that genetic factors provide a significant contribution to the pathogenesis and development of AD. In the past years, numerous genes implicated in this disease have been identified via genetic association studies on candidate genes or at the genome-wide level. However, in many cases, the roles of these genes and their interactions in AD are still unclear...
April 27, 2017: Alzheimer's Research & Therapy
https://www.readbyqxmd.com/read/28446149/effect-of-genetic-variants-and-traits-related-to-glucose-metabolism-and-their-interaction-with-obesity-on-breast-and-colorectal-cancer-risk-among-postmenopausal-women
#16
Su Yon Jung, Eric M Sobel, Jeanette C Papp, Zuo-Feng Zhang
BACKGROUND: Impaired glucose metabolism-related genetic variants and traits likely interact with obesity and related lifestyle factors, influencing postmenopausal breast and colorectal cancer (CRC), but their interconnected pathways are not fully understood. By stratifying via obesity and lifestyles, we partitioned the total effect of glucose metabolism genetic variants on cancer risk into two putative mechanisms: 1) indirect (risk-associated glucose metabolism genetic variants mediated by glucose metabolism traits) and 2) direct (risk-associated glucose metabolism genetic variants through pathways other than glucose metabolism traits) effects...
April 26, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28446055/investigational-drugs-for-nasopharyngeal-carcinoma
#17
Brigette B Y Ma, Edwin P Hui, Anthony T C Chan
Nasopharyngeal carcinoma (NPC) is endemic to Southern China and Asia and is etiologically associated with the Epstein Barr virus (EBV). Whole exome and genome sequencing (WES, WGS) studies of NPC have reported several actionable therapeutic targets, and that the mutational load of NPC maybe comparable to that of squamous head and neck cancer. These unique biological characteristics have been exploited as potential targets and a wide range of investigational drugs are being investigated in clinical trials. Area covered: This review focused on the latest clinical development of the most promising classes of investigational agents in the treatment of advanced NPC...
April 27, 2017: Expert Opinion on Investigational Drugs
https://www.readbyqxmd.com/read/28446001/a-post-genome-wide-association-study-validating-the-association-of-the-glycophorin-c-gene-with-serum-hemoglobin-level-in-pig
#18
Yang Liu, Zhengzheng Hu, Chen Yang, Shiwei Wang, Wenwen Wang, Qin Zhang
OBJECTIVE: This study aimed to validate the statistical evidence from the genome-wide association study (GWAS) as true-positive and to better understand the effects of the glycophorin C (GYPC) gene on serum hemoglobin traits. METHODS: Our initial GWAS revealed the presence of two single nucleotide polymorphisms (SNPs) (ASGA0069038 and ALGA0084612) for the hemoglobin concentration trait (HGB) in the 2.48 Mb region of SSC15. From this target region, GYPC was selected as a promising gene that associated with serum HGB traits in pigs...
May 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28445865/associations-between-lmo1-gene-polymorphisms-and-wilms-tumor-susceptibility
#19
Guo-Chang Liu, Zhen-Jian Zhuo, Shi-Bo Zhu, Jinhong Zhu, Wei Jia, Zhang Zhao, Jin-Hua Hu, Jing He, Feng-Hua Wang, Wen Fu
Wilms' tumor is the most common childhood renal malignancy. A genome-wide association study identified LIM domain only 1 (LMO1) as having oncogenic potential. We examined the associations between LMO1 gene polymorphisms and susceptibility to Wilms' tumor. In this hospital-based, case-control study, we recruited 145 children with Wilms' tumor and 531 cancer-free children. Four polymorphisms (rs110419 A>G, rs4758051 G>A, rs10840002 A>G and rs204938 A>G) were genotyped using Taqman methodology. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to measure the associations between selected polymorphisms and Wilms' tumor susceptibility...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#20
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
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